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9y51

PanDDA analysis -- Crystal Structure of Zika virus NS3 Helicase in complex with Z1563512128

Method: X-RAY DIFFRACTION D_max: 71.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y51
deposition_date	2025-09-04
last_revision	2025-09-17
title	PanDDA analysis -- Crystal Structure of Zika virus NS3 Helicase in complex with Z1563512128
keywords	zika, helicase, pandda, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	23.30 Å
rg_electron	22.27 Å
i0	42584500.00
molecular_weight	49526.0 kDa
excluded_volume	61670 Å³
envelope_volume	73118 Å³
shell_volume	26866 Å³
envelope_diameter	72.9 Å
shell_rg	29.75 Å
envelope_rg	22.41 Å
shape_rg	22.28 Å
total_rg	23.12 Å
total_atoms	3475
n_residues	435
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	71.1 Å
rg_real	23.17 Å
rg_real_error	0.37 Å
i0_real	4.2580e+07
i0_real_error	5.6560e+05
rg_reciprocal	23.21 Å
i0_reciprocal	42590000.0000
total_estimate	0.9110
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	28.5 Å
skewness	0.158
kurtosis	-0.539
angular_range	— – 0.3400 Å⁻¹
current_alpha	0.0000
highest_alpha	15660000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.998

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Zika virus NS3 helicase domain
formula_weight	48950.0 kDa
ec_number	3.6.4.13
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3850

MLKKKQLTVLDLHPGAGKTRRVLPEIVREAIKKRLRTVILAPTRVVAAEMEEALRGLPVRYMTTAVNVTHSGTEIVDLMCHATFTSRLLQPIRVPNYNLNIMDEAHFTDPSSIAARGYISTRVEMGEAAAIFMTATPPGTRDAFPDSNSPIMDTEVEVPERAWSSGFDWVTDHSGKTVWFVPSVRNGNEIAACLTKAGKRVIQLSRKTFETEFQKTKNQEWDFVITTDISEMGANFKADRVIDSRRCLKPVILDGERVILAGPMPVTHASAAQRRGRIGRNPNKPGDEYMYGGGCAETDEGHAHWLEARMLLDNIYLQDGLIASLYRPEADKVAAIEGEFKLRTEQRKTFVELMKRGDLPVWLAYQVASAGITYTDRRWCFDGTTNNTIMEDSVPAEVWTKYGEKRVLKPRWMDARVCSDHAALKSFKEFAAGKR

Source

organism	Zika virus
ncbi_taxonomy_id	64320
host_organism	Escherichia coli

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	(4S)-2-METHYL-2,4-PENTANEDIOL
formula_weight	118.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	N-[(2S)-2-hydroxypropyl]-N'-phenylurea
formula_weight	194.2 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	356

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6. Citations (1)

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length_a	53.690 Å
length_b	69.420 Å
length_c	57.260 Å
angle_alpha	90.00 °
angle_beta	92.11 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.730 Å
resolution_low	34.580 Å
r_factor	0.1762
r_work	0.1745
r_free	0.2133

fit	/app/data/saxs_computation/y5/9y51/9y51.fit
pddf	/app/data/pr_computation/y5/9y51/9y51.pr.out
profile	/app/data/saxs_computation/y5/9y51/9y51.dat